Research workbench
Structure of aggregatibacter actinomycetemcomitans macb bound to atpys (P21)
Analyse Structure of aggregatibacter actinomycetemcomitans macb bound to atpys (P21) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LIL
- Type
- protein
- Length
- 1,219 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Macrolide export ATP-BINDING/PERMEASE protein macb
- EC
- 3.6.3.-
- UniProt
- Q2EHL8
- Ligands
- ATP, MG
- Pockets
- 18 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Macrolide export ATP-BINDING/PERMEASE protein macb (EC 3.6.3.-) | protein | 615 | 48% helix, 18% strand | Q2EHL8 |
| B | Macrolide export ATP-BINDING/PERMEASE protein macb (EC 3.6.3.-) | protein | 604 | 49% helix, 19% strand | Q2EHL8 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 914 | 0.83 | 0.85 | 100 | ATP, MG |
| 2 | 913 | 0.73 | 0.77 | 79 | empty |
| 3 | 60 | 0.71 | 0.97 | 15 | empty |
| 4 | 242 | 0.68 | 0.85 | 31 | empty |
| 5 | 162 | 0.56 | 0.81 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 3122 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5LIL · Structure of Aggregatibacter actinomycetemcomitans MacB bound to ATPyS (P21) · the same entry in another collection · chain A against A, TM-score 1.00
- Q2EHL8 · AlphaFold monomer V2.0 prediction for macrolide export ATP- BINDING/PERMEASE protein macb… · a predicted model of the same protein · chain A against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q2EHL8
- Elsewhere: RCSB PDB 5LIL · PDBe 5LIL · UniProt Q2EHL8
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